Isoetes savatieri has traditionally been interpreted as being a uniform aquatic ranging from the southernmost regions of South America to the central Andes of Chile and Argentina. An examination of herbarium material supports the recognition of two taxa, a southern I. savatieri and a more northern I. chubutiana, from central Chile and Argentina. The latter taxon is hexaploid and described here as a new species. The morphology of these species suggest that they are sister species resulting from divergence following a polyploidy event. These species, and several other species pairs, provide the best and, to date, only examples of allopatric divergence in polyploid Isoetes.